The root of this issue is not so much with IE vs Firefox per se,
but with the "integration" that Microsoft has said so much about.

http://www.kb.cert.org/vuls/id/998297

IE is designed, for better or worse, to be a command shell for
the OS, and not merely a web browsing app. All of its problems are rooted
in this design philosophy. Because of this integration, it has an advantage over competitors
because features provided by activeX cannot be accessed by other peoples'
browsers. It is a brazen attempt to extend (violate) web standards to
freeze competitors out of the browser market.

They are hoping that users will be unable to conceptually distinguish
between the "browser" and the "desktop".

http://en.wikipedia.org/wiki/Active_Desktop

For those of us who remember using computers before there was
an internet, integration is just jargon, but for most users, there is
no distinction between "using the computer" and "going online".
They don't want to sacrifice the convenience of installing software
off a web page with one click.